plant genomes making database error

[cfz1998]

plant genomes making database error

[cfz1998]

Thank you!

[qiyunzhu]

Hello @cfz1998 Thanks for reporting this issue. This problem happened because your command didn't specify how many genomes will be sampled per taxonomic group (e.g., using --sample 1).

I have tweaked the code so that it defaults to containing all genomes, such that your current command will work. To update the program, you can do:

pip install --force-reinstall --no-cache-dir git+https://github.com/qiyunlab/HGTector.git

[cfz1998]

Hello @cfz1998 Thanks for reporting this issue. This problem happened because your command didn't specify how many genomes will be sampled per taxonomic group (e.g., using --sample 1).

I have tweaked the code so that it defaults to containing all genomes, such that your current command will work. To update the program, you can do:

pip install --force-reinstall --no-cache-dir git+https://github.com/qiyunlab/HGTector.git

Hi! qiyun
I find a new issue:

# The code:
hgtector database -o db_dir --cat plant,archaea,bacteria,fungi,protozoa --threads 32

Error message:

Database building started at 2022-09-14 10:51:27.131615.
Downloading NCBI taxonomy database... done.
Reading NCBI taxonomy database... done.
  Total number of TaxIDs: 2442723.
Downloading RefSeq assembly summary... done.
Reading RefSeq assembly summary... done.
  Total number of genomes: 272849.
Genome categories: plant, archaea, bacteria, fungi, protozoa
Downloading genome list per RefSeq category...
  plant: 154
  archaea: 1322
  bacteria: 1322
  fungi: 1322
  protozoa: 1322
Done.
  Total number of genomes in categories: 1476.
Filtering genomes...
Done.
Filtering genomes by taxonomy...
Done.
Total number of sampled genomes: 1476.
Downloading non-redundant genomic data from NCBI...
Traceback (most recent call last):
  File "/data/chaofan/miniconda/envs/hgtector/bin/hgtector", line 96, in <module>
    main()
  File "/data/chaofan/miniconda/envs/hgtector/bin/hgtector", line 35, in main
    module(args)
  File "/data/chaofan/miniconda/envs/hgtector/lib/python3.10/site-packages/hgtector/database.py", line152, in __call__
    self.download_genomes()
  File "/data/chaofan/miniconda/envs/hgtector/lib/python3.10/site-packages/hgtector/database.py", line622, in download_genomes
    makedirs(ldir, exist_ok=True)
  File "/data/chaofan/miniconda/envs/hgtector/lib/python3.10/os.py", line 225, in makedirs
    mkdir(name, mode)
FileExistsError: [Errno 17] File exists: 'db_dir/download/faa'

[cfz1998]

Hi! @qiyunzhu
When i download data for a query list. [count 1336]
It's only download the default nr protein(archaea bacteria fungi protozoa). [count 1322]
genbank.txt

[qiyunzhu]

Hi @cfz1998 I don't quite understand your last question. Can you elaborate?

[cfz1998]

你好！ 就是我通过-g 参数来构建数据库，提供的NCBI assembly accessions列表里包括了1336个物种。其中有1322个物种是属于(archaea bacteria fungi protozoa)，这1322个物种也是使用--default参数自动下载的，其他14个物种是一些植物。 但是hgtector只构建了1322个物种的数据库，并没有包括我额外添加的这14个植物物种。

[qiyunzhu]

@cfz1998 Most likely it was because the 14 additional species do not have certain metadata fields available, especially taxonomic classification, thus HGTector skipped those organisms. Currently, a workaround will be that you manually download the proteomes, and manually edit the genome.tsv file as well as the taxonomy files. This isn't easy though. In the future HGTector may support taxonomy-free analysis, but not now...

[cfz1998]

Thank you for your help! I will try other ways.

[cfz1998]

plant: 154

Hi！@qiyunzhu.
How to dispose this error?